Cell-based detection and differentiation of disease states

Abstract

The present invention provides a method for detecting and differentiating disease states with high sensitivity and specificity. The method allows for a determination of whether a cell-based sample contains abnormal cells and, for certain diseases, is capable of determining the histologic type of disease present. The method detects changes in the level and pattern of expression of the molecular markers in the cell-based sample. Panel selection and validation procedures are also provided.

What is claimed is:  
     
         1 . A panel for detecting a generic disease state or discriminating between specific disease states using cell-based diagnosis, comprising a plurality of probes each of which specifically binds to a marker associated with a generic or specific disease state, wherein the pattern of binding of the component probes of the panel to cells in a cytology specimen is diagnostic of the presence or specific nature of said disease state.  
     
     
         2 . The panel of  claim 1 , wherein said generic disease state is selected from the group consisting of cancer and infectious diseases.  
     
     
         3 . The panel of  claim 2 , wherein said cancer is selected from the group consisting of epithelial cell-based cancers, solid tumor-based cancers, secretory tumor based cancers, and blood based cancers.  
     
     
         4 . The panel of  claim 2  wherein said infectious disease is selected from the group consisting of cell-based diseases in which the infectious organism is a virus, bacterium, protozoan, parasite, or fungus.  
     
     
         5 . The panel of  claim 1 , wherein said panel is optimized by using weighting factors selected from the group consisting of cost, prevalence of a generic disease state in a geographic location, prevalence of a specific disease state in a geographic location, availability of probes and commercial considerations.  
     
     
         6 . The panel of  claim 1 , wherein each of said probes comprises a detectable label.  
     
     
         7 . The panel of  claim 6 , wherein said probes comprise antibodies.  
     
     
         8 . The panel of  claim 6 , wherein said label is selected from the group consisting of a chromophore, a fluorophore, a dye, a radioisotope and an enzyme.  
     
     
         9 . The panel of  claim 8 , wherein said label is a chromophore detected using electromagnetic radiation selected from the group consisting of beta rays, gamma rays, X rays, ultraviolet radiation, visible light, infrared radiation and microwaves.  
     
     
         10 . The panel of  claim 1 , wherein said pattern of binding is detected using photonic microscopy.  
     
     
         11 . The panel of  claim 10 , wherein said photonic microscopy utilizes at least one electromagnetic radiation selected from the group consisting of gamma rays, X rays, beta rays, ultraviolet radiation, visible light, infrared radiation and microwaves.  
     
     
         12 . The panel of  claim 1 , wherein said detecting is for sexually transmitted diseases and said discriminating is between chlamydia, trichomonas, gonorrhea, herpes and syphilis.  
     
     
         13 . A method of forming a panel for detecting a disease state or discriminating between disease states in a patient using cell-based diagnosis, comprising: 
 (a) determining the sensitivity and specificity of binding of probes each of which specifically binds to a member of a library of markers associated with a disease state; and    (b) selecting a limited plurality of said probes whose pattern of binding is diagnostic for the presence or specific nature of said disease state.    
     
     
         14 . The method of  claim 13 , wherein said determining comprises: 
 (a) separately contacting a histological or cytological sample from a patient known to be suffering from said disease and a histological or cytological sample from a patient known not to be suffering from said disease with each of said probes;    (b) measuring the amount of specific binding of each probe with its complementary disease marker at loci where said marker is known to be present in cells of said samples; and    (c) correlating each said amount with the presence or specific nature of said disease.    
     
     
         15 . The method of  claim 13 , wherein said selecting comprises one or more of statistical analytical methods, pattern recognition methods and neural network analysis.  
     
     
         16 . The method of  claim 13 , where said selecting comprises the use of weighting factors.  
     
     
         17 . A method of detecting a disease or discriminating between disease states comprising: 
 (a) contacting a cytological sample suspected of containing abnormal cells characteristic of a disease state with a panel according to  claim 1;  and    (b) detecting a pattern of binding of said probes that is diagnostic for the presence or specific nature of said disease state.    
     
     
         18 . The method of  claim 17 , wherein said cytological sample is a cellular sample collected from a body fluid, an epithelial cell-based organ system, a fine needle aspiration or a biopsy.  
     
     
         19 . The method of  claim 18 , wherein said cytological sample is sputum.  
     
     
         20 . A panel for detecting a generic disease state or discriminating between specific disease states using cell-based diagnosis, wherein said panel is formed according to the method of  claim 13 .  
     
     
         21 . The panel of  claim 1 , wherein said disease marker is selected from the group consisting of a morphologic biomarker, a genetic biomarker, a cell cycle biomarker, a molecular biomarker and a biochemical biomarker.  
     
     
         22 . The panel of  claim 3 , wherein said epithelial cell-based cancer is from the pulmonary, urinary, gastrointestinal or genital tract.  
     
     
         23 . The panel of  claim 3 , wherein said solid tumor-based cancer is selected from the group consisting of a sarcoma, breast cancer, pancreatic cancer, liver cancer, kidney cancer, thyroid cancer, and prostate cancer.  
     
     
         24 . The panel of  claim 3 , wherein said secretory tumor-based cancer is selected from the group consisting of a sarcoma, breast cancer, pancreatic cancer, liver cancer, kidney cancer, thyroid cancer, and prostate cancer.  
     
     
         25 . The panel of  claim 3 , wherein said blood-based cancer is selected from the group consisting of leukemia and lymphoma.  
     
     
         26 . The method of  claim 18 , wherein said body fluid is selected from the group consisting of blood, urine, spinal fluid and lymph.  
     
     
         27 . The method of  claim 18 , wherein said epithelial cell based organ system is selected from the group consisting of the pulmonary tract, the urinary tract, the genital tract and the gastrointestinal tract.  
     
     
         28 . The method of  claim 18 , wherein said final needle aspiration is from solid tissue types in organs and systems.  
     
     
         29 . The method of  claim 18 , wherein said biopsy is from solid tissue types in organs and systems.  
     
     
         30 . The method of  claim 28 , wherein said organs and systems are selected from the group consisting of breast, pancreas, liver, kidney, thyroid, bone marrow, muscle, prostate and lung.  
     
     
         31 . The panel of  claim 21 , wherein said morphologic biomarker is selected from the group consisting of DNA ploidy, MACs, and premalignant lesions.  
     
     
         32 . The panel of  claim 21 , wherein said genetic biomarker is selected from the group consisting of DNA adducts, DNA mutations and apoptotic indices.  
     
     
         33 . The panel of  claim 21 , wherein said cell cycle biomarker is selected from the group consisting of cellular proliferation markers, differentiation markers, regulatory molecules and apoptosis markers.  
     
     
         34 . The panel of  claim 21 , wherein said molecular biomarker or biochemical biomarker is selected from the group consisting of oncogenes, tumor suppressor genes, tumor antigens, growth factors and receptors, enzymes, proteins, prostaglandins and adhesion molecules.  
     
     
         35 . The method of  claim 29 , wherein said organs and systems are selected from the group consisting of breast, pancreas, liver, kidney, thyroid, bone marrow, muscle, prostate and lung.